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DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures

文献类型：期刊论文

作者Qiao, Yixuan1,2; Yang, Rui1,2; Liu, Yang1,2; Chen, Jiaxin2; Zhao, Lianhe2; Huo, Peipei2; Wang, Zhihao2; Bu, Dechao2; Wu, Yang2; Zhao, Yi1,2
刊名COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
出版日期2024-12-01
卷号23页码:617-625
关键词Information fusion Deep learning RNA -binding proteins In vivo RNA structures Motifs
ISSN号2001-0370
DOI10.1016/j.csbj.2023.12.040
英文摘要RNA -binding proteins (RBPs) are key post -transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high -throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein -RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two submodels to extract local motif -like information and long-term context information. We show that DeepFusion performs best compared with other cutting -edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBPbinding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
资助项目National Key R&D Program of China[2022YFC3500105] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA16021400] ; National Natural Science Foundation of China[82172864] ; National Natural Science Foundation of China[32070670] ; Innovation Fund from Institute of Computing Technology, CAS[E161080] ; Zhejiang Provincial Natural Science Foundation of China[LY21C060003] ; Beijing Natural Science Foundation Haidian Origination and Innovation Joint Fund[L222007]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
语种英语
WOS记录号WOS:001154337300001
出版者ELSEVIER
源URL[http://119.78.100.204/handle/2XEOYT63/38383]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Wu, Yang; Zhao, Yi
作者单位1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Res Ctr Ubiquitous Comp Syst, Inst Comp Technol, Beijing 100190, Peoples R China
推荐引用方式
GB/T 7714		 Qiao, Yixuan,Yang, Rui,Liu, Yang,et al. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures[J]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,2024,23:617-625.
APA Qiao, Yixuan.,Yang, Rui.,Liu, Yang.,Chen, Jiaxin.,Zhao, Lianhe.,...&Zhao, Yi.(2024).DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures.COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,23,617-625.
MLA Qiao, Yixuan,et al."DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures".COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 23(2024):617-625.

入库方式： OAI收割

来源：计算技术研究所

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